[gmx-users] Generating Entropy from Umbrella Sampling Data

Billy Williams-Noonan billy.williams-noonan at monash.edu
Wed Aug 17 02:55:22 CEST 2016


Justin,

Does *gmx distance* plot the distance between the COM of two index groups?

Billy

On 17 August 2016 at 10:50, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/16/16 8:28 PM, Billy Williams-Noonan wrote:
>
>> Thank you that is what I have been doing... :)
>>
>> My problem is that I don't have the average COM distance for each
>> simulation.  Yes I specify what distance I want in the .mdp settings, but
>> in the earlier umbrella windows our average COM distance deviates somewhat
>> from the distance set in the mdp settings.  So I need a reliable way of
>> getting an average COM distance to match the average energy output from
>> gmx
>> energy.
>>
>>
> This is the primary function of gmx distance.
>
> -Justin
>
>
> Best,
>>
>> Billy
>>
>>
>>
>> On 17 August 2016 at 00:28, David van der Spoel <spoel at xray.bmc.uu.se>
>> wrote:
>>
>> On 16/08/16 16:02, Billy Williams-Noonan wrote:
>>>
>>> Hi David,
>>>>
>>>> Yes it's a basic question...  More about my inexperience with Gromacs
>>>> than
>>>> anything (and maybe my chemistry background, not my math background...)
>>>>
>>>> Gmx energy gives an enthalpy against time in the .xvg output, am trying
>>>> to
>>>> translate that to enthalpy against pull distance.
>>>>
>>>> What I had been doing was taking the mean state from each distribution
>>>> in
>>>> the histo.xvg output, matching that up to a corresponding pull distance,
>>>> and assuming that the mean enthalpy from gmx energy also matched up to
>>>> that
>>>> pull distance.
>>>>
>>>> Is there a better way?
>>>>
>>>> You want to average over all conformations in the simulation, same as
>>> you
>>> do in the PMF. So for each distance you compute the average energy with
>>> gmx
>>> energy and plot it.
>>>
>>>
>>> Best regards,
>>>>
>>>> Billy
>>>> On Tuesday, 16 August 2016, David van der Spoel <spoel at xray.bmc.uu.se>
>>>> wrote:
>>>>
>>>> On 16/08/16 09:28, Billy Williams-Noonan wrote:
>>>>
>>>>>
>>>>> Hi David,
>>>>>
>>>>>>
>>>>>>    I was wondering if you had any advice on how to plot enthalpy
>>>>>> against
>>>>>> COM pulling distance in the same manner that you have in *Figure 4*
>>>>>> above?
>>>>>>
>>>>>> Maybe I don't understand the question, but I'd say you just plot the
>>>>>>
>>>>> potential energy (from the energy file) with error bar for each data
>>>>> point
>>>>> and normalize to zero at infinite distance.
>>>>>
>>>>>
>>>>>    Best regards,
>>>>>>
>>>>>> Billy
>>>>>>
>>>>>> On 2 August 2016 at 18:15, Billy Williams-Noonan <
>>>>>> billy.williams-noonan at monash.edu> wrote:
>>>>>>
>>>>>> Yes we've noticed that.  Our error estimates for enthalpy are quite
>>>>>> high
>>>>>>
>>>>>> compared to the free energies at each umbrella window.
>>>>>>>
>>>>>>> On 2 August 2016 at 17:10, David van der Spoel <spoel at xray.bmc.uu.se
>>>>>>> >
>>>>>>> wrote:
>>>>>>>
>>>>>>> On 20/07/16 02:51, Billy Williams-Noonan wrote:
>>>>>>>
>>>>>>>
>>>>>>>> Hi David,
>>>>>>>>
>>>>>>>>
>>>>>>>>>   Thank you...!  To clarify, in Figure 4 of the paper referred to,
>>>>>>>>> you
>>>>>>>>> seem
>>>>>>>>> to have plotted the enthalpy of each frame against the COM pull
>>>>>>>>> distance
>>>>>>>>> and then used those values and the PMFs at each point to compute
>>>>>>>>> -TdS ?
>>>>>>>>> If
>>>>>>>>> so I might do something similar.
>>>>>>>>>
>>>>>>>>> Yes indeed.
>>>>>>>>>
>>>>>>>>>
>>>>>>>> The only problem is that enthalpies converge much more slowly than
>>>>>>>> free
>>>>>>>> energies.
>>>>>>>>
>>>>>>>>
>>>>>>>> Billy
>>>>>>>>
>>>>>>>>
>>>>>>>>> On Wednesday, 20 July 2016, David van der Spoel <
>>>>>>>>> spoel at xray.bmc.uu.se>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> On 19/07/16 12:22, Billy Williams-Noonan wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi David,
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>   Thank you for all your responses on here. :)  We'll have to make
>>>>>>>>>>> you
>>>>>>>>>>> an
>>>>>>>>>>> author if/when this gets published haha.
>>>>>>>>>>>
>>>>>>>>>>>    Will try to use gmx covar / anaeig at every point but my
>>>>>>>>>>> system
>>>>>>>>>>> has
>>>>>>>>>>> 30,000 atoms so it may not be completely faesible to get an
>>>>>>>>>>> accurate
>>>>>>>>>>> value
>>>>>>>>>>> for the system (same problem as before).
>>>>>>>>>>>
>>>>>>>>>>> You only do this for the biomolecules separately, not the water.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>    Could I simply use gmx energy and get an ensemble average
>>>>>>>>>> enthalpy
>>>>>>>>>>
>>>>>>>>>> for
>>>>>>>>>>> each point?  Then I can use the Gibbs free energy equation to
>>>>>>>>>>> solve
>>>>>>>>>>> for
>>>>>>>>>>> entropy.
>>>>>>>>>>>
>>>>>>>>>>> Yes, this is what we did in the paper :).
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>> Billy
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Tuesday, 19 July 2016, David van der Spoel <
>>>>>>>>>>> spoel at xray.bmc.uu.se>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>> On 19/07/16 09:47, Billy Williams-Noonan wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Hi All,
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>    I have seen papers where enthalpy and entropy are plotted
>>>>>>>>>>>>
>>>>>>>>>>>>> against
>>>>>>>>>>>>> the
>>>>>>>>>>>>> distance of a steered MD pull and am wanting to do something
>>>>>>>>>>>>> similar.
>>>>>>>>>>>>>
>>>>>>>>>>>>>    I have run a steered MD simulation pulling a cyclic peptide
>>>>>>>>>>>>> out
>>>>>>>>>>>>> of
>>>>>>>>>>>>> the
>>>>>>>>>>>>> binding site and the PMF calculation with *gmx wham* was in
>>>>>>>>>>>>> reasonable
>>>>>>>>>>>>> agreement with experiment.  to
>>>>>>>>>>>>>
>>>>>>>>>>>>> We have published stuff like that (e.g. J. Chem. Theor.
>>>>>>>>>>>>> Comput. 9
>>>>>>>>>>>>> pp.
>>>>>>>>>>>>>
>>>>>>>>>>>>> 4542-4551 (2013)http://pubs.acs.org/doi/abs/10.1021/ct400404q)
>>>>>>>>>>>>>
>>>>>>>>>>>>> There are two main ways of doing this, rerunning the PMF at
>>>>>>>>>>>> different
>>>>>>>>>>>> temperatures and using the Van 't Hoff equation, or computing
>>>>>>>>>>>> the
>>>>>>>>>>>> entropy
>>>>>>>>>>>> (approximately) using gmx covar / gmx anaeig for each of the
>>>>>>>>>>>> species.
>>>>>>>>>>>>
>>>>>>>>>>>> gmx sham is just for plotting an energy landscape, e.g.
>>>>>>>>>>>> J. Mol. Biol. 354 pp. 173-183 (2005)
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>    What I would like now is plot the entropy and enthalpy
>>>>>>>>>>>> components
>>>>>>>>>>>>
>>>>>>>>>>>> against the pull distance.  I stumbled across *gmx sham* and
>>>>>>>>>>>> would
>>>>>>>>>>>>
>>>>>>>>>>>> like
>>>>>>>>>>>>> to
>>>>>>>>>>>>> use that, however I can't find any information on how to use it
>>>>>>>>>>>>> online.  I
>>>>>>>>>>>>> found these posts on online forums but have found them to be
>>>>>>>>>>>>> unhelpful
>>>>>>>>>>>>> (I'm
>>>>>>>>>>>>> sure it makes sense, it's just I am more of a chemist than a
>>>>>>>>>>>>> mathematician).
>>>>>>>>>>>>>
>>>>>>>>>>>>> *
>>>>>>>>>>>>>
>>>>>>>>>>>>> http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/
>>>>>>>>>>>>> hmlPKJSt/how-to-use-g-sham
>>>>>>>>>>>>> <
>>>>>>>>>>>>>
>>>>>>>>>>>>> http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/
>>>>>>>>>>>>> hmlPKJSt/how-to-use-g-sham
>>>>>>>>>>>>>
>>>>>>>>>>>>> *
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> *http://comments.gmane.org/gmane.science.biology.gromacs.use
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> r/64417
>>>>>>>>>>>>> <http://comments.gmane.org/gmane.science.biology.gromacs.use
>>>>>>>>>>>>> r/64417
>>>>>>>>>>>>>
>>>>>>>>>>>>> *
>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>    I have also looked through the Gromacs 5.1.2 manual and
>>>>>>>>>>>>> cannot
>>>>>>>>>>>>> find
>>>>>>>>>>>>> anything on *gmx sham*.
>>>>>>>>>>>>>
>>>>>>>>>>>>> *http://manual.gromacs.org/documentation/5.1.2/manual-5.1.2.
>>>>>>>>>>>>> pdf
>>>>>>>>>>>>> <http://manual.gromacs.org/documentation/5.1.2/manual-5.1.2.
>>>>>>>>>>>>> pdf
>>>>>>>>>>>>>
>>>>>>>>>>>>>> *
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>    Could someone please let me know the exact commands I need
>>>>>>>>>>>>> to
>>>>>>>>>>>>> use
>>>>>>>>>>>>> with
>>>>>>>>>>>>> *gmx
>>>>>>>>>>>>> sham i*n order to plot entropy and enthalpy against the pull
>>>>>>>>>>>>> distance?
>>>>>>>>>>>>>
>>>>>>>>>>>>>    Kind regards,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Billy
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>>
>>>>>>>>>>>>> David van der Spoel, Ph.D., Professor of Biology
>>>>>>>>>>>>>
>>>>>>>>>>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>>>>>>>>>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>>>>>>>>>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>>>>>>>>>>>> --
>>>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>>>
>>>>>>>>>>>> * Please search the archive at
>>>>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
>>>>>>>>>>>> before
>>>>>>>>>>>> posting!
>>>>>>>>>>>>
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>>>>>>>>>>>>
>>>>>>>>>>>> * For (un)subscribe requests visit
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>>>>>>>>>>>> -users
>>>>>>>>>>>> or
>>>>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> David van der Spoel, Ph.D., Professor of Biology
>>>>>>>>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>>>>>>>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>>>>>>>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>>>>>>>>>> --
>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>
>>>>>>>>>> * Please search the archive at
>>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
>>>>>>>>>> before
>>>>>>>>>> posting!
>>>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>> * For (un)subscribe requests visit
>>>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx
>>>>>>>>>> -users
>>>>>>>>>> or
>>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>> David van der Spoel, Ph.D., Professor of Biology
>>>>>>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>>>>>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>>>>>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>>>>>>>> --
>>>>>>>> Gromacs Users mailing list
>>>>>>>>
>>>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>>>>>
>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>
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>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>>> or
>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>>>> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
>>>>>>>
>>>>>>> *LinkedIn Profile
>>>>>>> <http://www.linkedin.com/profile/preview?locale=en_US&trk=
>>>>>>> prof-0-sb-preview-primary-button>
>>>>>>> **|*   +61420 382 557
>>>>>>>
>>>>>>> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
>>>>>>> Royal Parade, Parkville, 3052
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>> David van der Spoel, Ph.D., Professor of Biology
>>>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>
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>>>>>
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>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
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>>>
>>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
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-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

*LinkedIn Profile
<http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052


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